Lucas et al. figures

Figure 1

Chikungunya virus is found in MARCO-expressing floor lymphatic endothelial cells in the draining lymph node at 8 hpi

  1. UMAP projection shows the fraction of counts aligning to the CHIKV genome for the 8 hpi timepoint.
  2. UMAP projection shows CHIKV+ cells (>0 CHIKV counts) for the 8 hpi timepoint.
  3. CHIKV counts are shown for cell types with >50 cells for the 8 hpi CHIKV-infected sample.
  4. The fraction of cells identified as CHIKV+ is shown for each cell type for the 8 hpi timepoint.
  5. MARCO expression is shown for fLECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV low or CHIKV high. P values were calculated using a two-sided Wilcoxon rank-sum test with Bonferroni correction. In the boxplot, the central lines, the box limits, and the whiskers represent medians, the interquartile range (IQR), and min/max values that are not outliers, respectively. Outliers are shown as points and include any values that are more than 1.5× IQR away from the box.
  6. Madcam1 expression is shown for fLECs as described in E.


Figure S1

CHIKV may target MARCO-expressing LECs for infection

CHIKV signal

  1. UMAP projection shows annotated cell types for the 24 hpi timepoint.
  2. UMAP projection shows CHIKV sgRNA ratio (sgRNA counts / 5’ counts) for the 24 hpi timepoint.
  3. The fraction of cells identified as CHIKV-high is shown for each cell type for the 24 hpi timepoint.
  4. CHIKV sgRNA ratio is shown for cells with >0 sgRNA counts and >0 5’ counts. Cell types with >10 cells are shown.
  5. The correlation between CHIKV sgRNA ratio and QC metrics is shown for CHIKV-high cells.


Cell type annotation

  1. The correlation between annotated LEC subsets and reference data is shown for the 8 hpi and 24 hpi timepoint.
  2. The expression of select marker genes is shown for the 8 hpi and 24 hpi timepoints.


Figure 5

IN PROGRESS


P01 figures

Figure 1


Figure 2

  1. MARCO expression is shown for LEC and FRC subtypes for the 8 hpi and 24 hpi timepoints.
  2. Mxra8 expression is shown as described in A.


Figure 3

  • Using scRNAseq, we found that during WT CHIKV infection, expression of CCL21 (attracts CCR7+ cells) and IL-7 (supports T cell proliferation and survival) were reduced in both LECs and FRCs
  • In addition, expression of CXCL13, which recruits CXCR5 expressing B cells and Tfh cells to B cell follicles and GCs, was specifically reduced in FDCs.
  • Moreover, MRCs that are positioned at the edge of B cell follicles adjacent to the SCS, and are also an important source of CXCL13, were undetectable by scRNAseq in the LNs of mice infected with WT CHIKV at 24 hpi. MRCs were detected in LNs of mock-infected mice and CHIKV-infected mice at 8 hpi, suggesting these cells are lost or damaged by 24 h after CHIKV infection.
  1. CCL21 and IL7 expression is shown for mock and CHIKV-infected samples from the 24 hpi timepoint. * p < 0.01, ** p < 0.001, *** p < 0.0001.
  2. CXCL13 expression is shown for FRC subsets from mock and CHIKV-infected samples from the 24 hpi timepoint.
  3. The proportion of FRCs belonging to different subsets is shown for the 8 hpi and 24 hpi timepoints.
  4. The proportion of FRCs belonging to different subsets is shown for mock and CHIKV-infected samples from the 24 hpi timepoint. The height of each bar graph shows the mean for 3 biological replicates, error bars show the standard deviation. p-values were calculated using a two-sample t-test, p-values < 0.05 are shown above each set of bar graphs.